Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (Mnase-Seq)

Embryonic stem cells (ESCs) and induced-pluripotent stem cells (iPSCs) self-renew and differentiate into an array of cell types in vitro and in vivo. A complex network of genetic and epigenetic pathways regulates the self-renewal and differentiation of these pluripotent cells, and the structure and covalent modifications of chromatin play a prominent role in this process. We examine nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach that enabled the identification of regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. The majority of changes in nucleosomal signatures that occur in differentiation are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of pluripotency and likely identify key regulatory regions that play a role in determining cell identity. Micrococcal nuclease digestion of chromatin in crosslinked cells was followed by high throughput sequencing. These experiments were carried out in four mouse cell types: embryonic stem cells, induced pluripotent stem cells, somatic tail-tip fibroblasts and liver, and three human cell types: H1-OGN embryonic stem cells, H1-OGN induced pluripotent stem cells, and fibroblasts differentiated from H1-OGN ESCs. At least two replicates performed with each cell type were sequenced.